Beauchamp:ROIanalysis: Difference between revisions
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Inferior frontal gyrus 285, 505 | Inferior frontal gyrus 285, 505 | ||
Superior temporal sulcus 513 | Superior temporal sulcus 513 | ||
To use these parcellations, first copy over the parcellation files from the SUMA folder: | |||
cd /Volumes/data9/surfaces/last_name/subjID/SUMA/ | |||
cp lh.aparc.a2005s.annot.1D.roi /Volumes/data1/UT/{$ec}/afni | |||
cp rh.aparc.a2005s.annot.1D.roi /Volumes/data1/UT/{$ec}/afni | |||
cd /Volumes/data1/UT/{$ec}/afni | |||
The, convert them into BRIK files for AfNI analysis: | |||
3dSurf2Vol -spec /Volumes/data9/surfaces/netek_anne/HO/SUMA/both.spec -surf_A lh.smoothwm.asc \ | |||
-grid_parent {$ec}v1mr+orig -sv {$ec}_SurfVol_Alnd_Exp+orig -map_func max -prefix L_parc -sdata_1D lh.aparc.a2005s.annot.1D.roi | |||
3dSurf2Vol -spec /Volumes/data9/surfaces/netek_anne/HO/SUMA/both.spec -surf_A rh.smoothwm.asc \ | |||
-grid_parent {$ec}v1mr+orig -sv {$ec}_SurfVol_Alnd_Exp+orig -map_func max -prefix R_parc -sdata_1D rh.aparc.a2005s.annot.1D.roi |
Revision as of 08:21, 23 May 2011
If you would like to compare activity across subjects in threshold-defined areas, an ROI analysis may be right for you!
For example, we may be interested in comparing amplitude of activity in auditory cortex during different types of speech stimuli in people with different behavioral characteristics. While we could use a group whole-brain analysis to see if there are any voxels in a combined map within auditory cortex that show a differential response, it may be better to separately define each auditory ROI in each subject using strict and reproducible criteria, such as T stat > 3.
To facilitate this process, the surfaces in SUMA come already parcellated into useful regions. With the parcellation, each anatomical region is assigned a value (same in left and right hemisphere). So, for each subject, we can find active areas within these anatomical locations to use as ROIs. Depending on when the surface was made, the parcellation is done either with a 2005s or 2009s atlas.
Here are the parcellation values corresponding to 5 regions of interest using the 2005s atlas:
Auditory cortex 33, 81 Extrastriate visual cortex (V5/MT) 60 Fusiform gyrus 17, 63 Inferior frontal gyrus 6, 72 Superior temporal sulcus 80
And for the 2009s atlas:
Auditory cortex 466, 514 Extrastriate visual cortex (V5/MT) 493 Fusiform gyrus 450 Inferior frontal gyrus 285, 505 Superior temporal sulcus 513
To use these parcellations, first copy over the parcellation files from the SUMA folder:
cd /Volumes/data9/surfaces/last_name/subjID/SUMA/ cp lh.aparc.a2005s.annot.1D.roi /Volumes/data1/UT/{$ec}/afni cp rh.aparc.a2005s.annot.1D.roi /Volumes/data1/UT/{$ec}/afni cd /Volumes/data1/UT/{$ec}/afni
The, convert them into BRIK files for AfNI analysis:
3dSurf2Vol -spec /Volumes/data9/surfaces/netek_anne/HO/SUMA/both.spec -surf_A lh.smoothwm.asc \ -grid_parent {$ec}v1mr+orig -sv {$ec}_SurfVol_Alnd_Exp+orig -map_func max -prefix L_parc -sdata_1D lh.aparc.a2005s.annot.1D.roi
3dSurf2Vol -spec /Volumes/data9/surfaces/netek_anne/HO/SUMA/both.spec -surf_A rh.smoothwm.asc \ -grid_parent {$ec}v1mr+orig -sv {$ec}_SurfVol_Alnd_Exp+orig -map_func max -prefix R_parc -sdata_1D rh.aparc.a2005s.annot.1D.roi